I think flawed masterpiece works for me. Obviously the "masterpiece" part is very subjective, but the funny thing I've noticed is that there's no consensus on what the major flaws are, or strengths for that matter (except maybe cinematography...most seem to agree this is a major strength. Even the best performance in the film is in dispute.). I've seen various people cite Acts 1, 2 and 3 as the source of the film's problems, just as I've hear others praise each of the 3 acts as the film's strongest. Similarly to how you'll hear arguments for Batman Begins, The Dark Knight and The Dark Knight Rises being the strongest film of the trilogy. Which I consider Acts 1, 2 and 3 of a larger movie.

And yeah, it's cool that TDK influenced Skyfall. I always thought there was somewhat of a parallel between BB and Casino Royale, both being modern and gritty re-imaginings of their title character (that also were also origin tales and attempted to get back in touch with the source material).